scDiffCom

Differential Analysis of Intercellular Communication from scRNA-Seq Data

v1.2.0 · Oct 14, 2025 · MIT + file LICENSE

Description

Analysis tools to investigate changes in intercellular communication from scRNA-seq data. Using a Seurat object as input, the package infers which cell-cell interactions are present in the dataset and how these interactions change between two conditions of interest (e.g. young vs old). It relies on an internal database of ligand-receptor interactions (available for human, mouse and rat) that have been gathered from several published studies. Detection and differential analyses rely on permutation tests. The package also contains several tools to perform over-representation analysis and visualize the results. See Lagger, C. et al. (2023) <doi:10.1038/s43587-023-00514-x> for a full description of the methodology.

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CRAN Check Status

1 ERROR

1 NOTE

12 OK

Show all 14 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	ERROR	4.2s
r-devel-linux-x86_64-debian-gcc	OK	286.4s
r-devel-linux-x86_64-fedora-clang	OK	611.7s
r-devel-linux-x86_64-fedora-gcc	OK	690.9s
r-devel-macos-arm64	OK	81s
r-devel-windows-x86_64	OK	320s
r-oldrel-macos-arm64	NOTE
r-oldrel-macos-x86_64	OK	305s
r-oldrel-windows-x86_64	OK	427s
r-patched-linux-x86_64	OK	388.1s
r-release-linux-x86_64	OK	389s
r-release-macos-arm64	OK
r-release-macos-x86_64	OK	332s
r-release-windows-x86_64	OK	309s

Check details (14 non-OK)

ERROR r-devel-linux-x86_64-debian-clang

package dependencies

Package required but not available: ‘DelayedArray’

Packages suggested but not available for checking:
  'biomaRt', 'GOSemSim', 'KEGGREST', 'ontoProc', 'rrvgo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

OK r-devel-linux-x86_64-debian-gcc

OK r-devel-linux-x86_64-fedora-clang

OK r-devel-linux-x86_64-fedora-gcc

OK r-devel-macos-arm64

OK r-devel-windows-x86_64

NOTE r-oldrel-macos-arm64

dependencies in R code

Error in py_module_import(module, convert = convert) : 
  ModuleNotFoundError: No module named 'owlready2'
Run `reticulate::py_last_error()` for details.
Using Python: /Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/bin/python3.9
Creating virtual environment 'r-owlready2' ... 
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/pkgbuild/.virtualenvs/r-owlready2/lib/python3.9/site-packages (21.2.4)
Collecting pip
  Using cached pip-25.2-py3-none-any.whl (1.8 MB)
Collecting wheel
  Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Requirement already satisfied: setuptools in /Users/pkgbuild/.virtualenvs/r-owlready2/lib/python3.9/site-packages (58.0.4)
Collecting setuptools
  Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 58.0.4
    Uninstalling setuptools-58.0.4:
      Successfully uninstalled setuptools-58.0.4
  Attempting uninstall: pip
    Found existing installation: pip 21.2.4
    Uninstalling pip-21.2.4:
      Successfully uninstalled pip-21.2.4
Successfully installed pip-25.2 setuptools-80.9.0 wheel-0.45.1
Virtual environment 'r-owlready2' successfully created.
Using virtual environment 'r-owlready2' ...
Collecting owlready2
  Downloading owlready2-0.48.tar.gz (27.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 27.3/27.3 MB 3.8 MB/s  0:00:07
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Building wheels for collected packages: owlready2
  Building wheel for owlready2 (pyproject.toml): started
  Building wheel for owlready2 (pyproject.toml): finished with status 'done'
  Created wheel for owlready2: filename=owlready2-0.48-cp39-cp39-macosx_11_0_universal2.whl size=23084262 sha256=5003cdf853da3e248914c7f9ae4bbcefcc629037538c6cd9acfa152a2c2e2ee8
  Stored in directory: /Users/pkgbuild/Library/Caches/pip/wheels/70/6f/5c/2e8a43efa7697b1bd04085d4e8d97a82b19e4ee37c710a9f7b
Successfully built owlready2
Installing collected packages: owlready2
Successfully installed owlready2-0.48

OK r-oldrel-macos-x86_64

OK r-oldrel-windows-x86_64

OK r-patched-linux-x86_64

OK r-release-linux-x86_64

OK r-release-macos-arm64

OK r-release-macos-x86_64

OK r-release-windows-x86_64

Check History

ERROR 12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 9, 2026

ERROR r-devel-linux-x86_64-debian-clang

package dependencies

Package required but not available: ‘DelayedArray’

Packages suggested but not available for checking:
  'biomaRt', 'GOSemSim', 'KEGGREST', 'ontoProc', 'rrvgo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

NOTE r-oldrel-macos-arm64

dependencies in R code

Error in py_module_import(module, convert = convert) : 
  ModuleNotFoundError: No module named 'owlready2'
Run `reticulate::py_last_error()` for details.
Using Python: /Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/bin/python3.9
Creating virtual environment 'r-owlready2' ... 
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/pkgbuild/.virtualenvs/r-owlready2/lib/python3.9/site-packages (21.2.4)
Collecting pip
  U

Dependency Network

Version History

new 1.2.0 Mar 9, 2026